First EcoChip to Track Soil Fungi Activity Rapidly and Cheaply

on February 11, 2012 12:02 PM EST

Fungus Activity in Eco Systems
Dr. Alfons R. Weig, leboratory for DNA-analytics and eco-informatics, and Dr. Derek Peršoh, Department of Mycology at University of Bayreuth (Photo: Chr. Wißler)

Scientists of the University of Bayreuth succeeded in developing modern chip technology to ecosystem research applications. Their new 'EcoChip' allows for a very broad screening for fungi and their functions.

In almost all ecosystems like forest and farmland fungi play a vital role. They decompose about 90 percent of all dead biomass and reintroduce it into the cycle of matter.

In an ecosystem different fungus species take on special roles and interact with each other. So far analyzing these this in all its breadth was not possible, because existing technologies could not provide sufficient tools. But now a an 'EcoChip' developed by biologists from Bayreuth will enable researchers to study this directly.

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The chip can screen soil samples for the contained fungus species. All extracted nucleic acids from a given sample are dyed and exposed to the micro array. The ones matching with sequences present on the array will stick and provide a patter, which can be analyzed.

This will allow to screen for many of the currently known 46,000 species of fungi and also give insight into their metabolic activity. The chip uses RNA instead of DNA, which allows to analyze the metabolic activity rather than to only identify the species present.

DNA comprises the complete set of genes of one organism, whereas RNA only is present in a cell, if the cell currently produces the respective protein related to this gene.

Before similar results could only be obtained by high throughput sequencing, which was already successfully used in genetic diagnostics, but would be far too expensive for the breadth of molecular ecological studies.

The original article was published in "Microarrays" by Prof. Dr. Gerhard Rambold and his team of Bayreuth's Mycology Department.

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